10-87933183-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PP2PP3PM2_SupportingBS3_Supporting
This summary comes from the ClinGen Evidence Repository: NM_000314.8(PTEN):c.424C>T (p.Arg142Trp) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.1.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).BS3_P: Well-established functional studies show no deleterious effect: Phosphatase activity >0 (score of this variant = 0.45) per Mighell et al. 2018 (PMID:29706350). PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.PP3: REVEL score > 0.7 (score of this variant = 0.716).PM2_P: Absent in gnomAD. Although this variant has been observed de novo in published literature (PMID 38335860) and internal laboratory cases, many of these patients and several others did not have features consistent with PTEN Hamartoma Tumor syndrome (PMID 26534844). This variant occurs as a CpG dinucleotide site; such sites have an increased rate of spontaneous deamination leading to de novo mutation (PMID 16570853). We believe that de novo observations of this variant are most likely incidental findings due to the hypermutable nature of this nucleotide position, and are not awarding de novo criteria as evidence towards pathogenicity given the inconsistent phenotypes present. LINK:https://erepo.genome.network/evrepo/ui/classification/CA000455/MONDO:0017623/003
Frequency
Consequence
NM_000314.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTEN | NM_000314.8 | c.424C>T | p.Arg142Trp | missense_variant | 5/9 | ENST00000371953.8 | |
PTEN | NM_001304717.5 | c.943C>T | p.Arg315Trp | missense_variant | 6/10 | ||
PTEN | NM_001304718.2 | c.-327C>T | 5_prime_UTR_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTEN | ENST00000371953.8 | c.424C>T | p.Arg142Trp | missense_variant | 5/9 | 1 | NM_000314.8 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251366Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135866
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461664Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727140
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
PTEN hamartoma tumor syndrome Uncertain:2
Uncertain significance, reviewed by expert panel | curation | Clingen PTEN Variant Curation Expert Panel, Clingen | May 17, 2024 | NM_000314.8(PTEN):c.424C>T (p.Arg142Trp) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.1.0). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). BS3_P: Well-established functional studies show no deleterious effect: Phosphatase activity >0 (score of this variant = 0.45) per Mighell et al. 2018 (PMID: 29706350). PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. PP3: REVEL score > 0.7 (score of this variant = 0.716). PM2_P: Absent in gnomAD. Although this variant has been observed de novo in published literature (PMID 38335860) and internal laboratory cases, many of these patients and several others did not have features consistent with PTEN Hamartoma Tumor syndrome (PMID 26534844). This variant occurs as a CpG dinucleotide site; such sites have an increased rate of spontaneous deamination leading to de novo mutation (PMID 16570853). We believe that de novo observations of this variant are most likely incidental findings due to the hypermutable nature of this nucleotide position, and are not awarding de novo criteria as evidence towards pathogenicity given the inconsistent phenotypes present. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2023 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 142 of the PTEN protein (p.Arg142Trp). This variant is present in population databases (rs746152219, gnomAD 0.0009%). This missense change has been observed in individual(s) with Cowden syndrome, breast and/or ovarian cancer and endometrial cancer (PMID: 16506206, 25669429, 26534844). ClinVar contains an entry for this variant (Variation ID: 197662). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PTEN protein function. Experimental studies have shown that this missense change affects PTEN function (PMID: 29785012). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 13, 2023 | Observed in at least one individual reported to meet Cowden syndrome or relaxed Cowden syndrome-like criteria (Nizialek et al., 2015); Reported as a variant of uncertain significance in at least one individual with familial breast cancer whose history was not suggestive of Cowden syndrome (Li et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28984400, 15492994, 17924977, 21470976, 16506206, 15923161, 29706350, 29785012, 23116406, 32384322, 33879063, 35338148, 28178681, 25669429, 26534844, 24475377) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 27, 2014 | - - |
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Apr 24, 2023 | This missense variant replaces arginine with tryptophan at codon 142 of the PTEN protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with Cowden and Cowden-like syndrome and multiple unaffected family members (PMID: 25669429), in an individual with a personal or family history of breast/ovarian cancer (PMID: 26534844), and in two individuals with endometrial cancer (PMID: 16506206). This variant has been identified in 1/251366 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The p.R142W variant (also known as c.424C>T), located in coding exon 5 of the PTEN gene, results from a C to T substitution at nucleotide position 424. The arginine at codon 142 is replaced by tryptophan, an amino acid with dissimilar properties. This variant has been detected in a cohort of patients who met clinical diagnostic criteria for Cowden syndrome (CS) or relaxed clinical diagnostic criteria for CS-like (Nizialek EA et al. Eur. J. Hum. Genet., 2015 Nov;23:1538-43). This variant has also been detected in a single family with a history of breast and/or ovarian cancer (Li J et al. J. Med. Genet., 2016 Jan;53:34-42). In a massively parallel functional assay using a humanized yeast model, lipid phosphatase activity for this variant was functionally neutral (Mighell TL et al. Am J Hum Genet, 2018 05;102:943-955). This variant demonstrated low intracellular protein abundance on one multiplex functional assay (Matreyek KA et al. Nat Genet, 2018 06;50:874-882). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Cowden syndrome 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Sep 27, 2023 | This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 29785012]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [Myriad internal data]. - |
Autistic behavior;C2243051:Macrocephaly;C4022738:Neurodevelopmental delay Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Jun 21, 2021 | ACMG classification criteria: PM2 moderate, PP2 supporting, PP3 supporting - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at